[ensembl-dev] getting the entrez gene id from an ensembl record

[Andreas Kahari]

People,

Do you think that get_all_xrefs() is a good alias name for
get_all_DBLinks()?  And can we use get_all_object_xrefs() (i.e. "get all
xrefs from this object, not from its constituent parts") as an alias for
get_all_DBEntries()?

Any better suggestions?

We're thinking about how to make it easier to use these methods, and how
to speed up the current get_all_DBLinks() method (which is non-trivial
due to the size of the xref table).  This will hopefully have some sort
of effect in release 62.

Regards,
Andreas

On Thu, Dec 02, 2010 at 10:05:45AM +0000, Glenn Proctor wrote:
> Hi
> 
> These are all good points - for release 61 we'll add methods that are
> aliases of get_all_DBLinks/Entries but have more intuitive names.
> 
> Glenn.
> 
> 
> On Thu, Dec 2, 2010 at 9:53 AM, Patrick Meidl <pmeidl at cemm.oeaw.ac.at> wrote:
> > On Thu, Dec 02 2010, Andy Jenkinson <andy.jenkinson at ebi.ac.uk> wrote:
> >
> >> > On Thu, Dec 02 2010, ian Longden <ianl at ebi.ac.uk> wrote:
> >> >
> >> >> Use $gene->get_all_DBLinks as this gets the external database
> >> >> references on the transcripts and translations of the gene too.
> >> >>
> >> >> DBEntries only gets the ones attached to the gene directly.
> >>
> >> Also, whether something is attached to a gene or transcript is not
> >> always intuitive: as I understand it, it depends on how the mapping
> >> was done, not the logical data model relationships. You have to know
> >> the internal data model before you can use it. For example, why is an
> >> EntrezGene not a gene-related record?
> >
> > exactly. I therefore think that what is now called get_all_DBLinks()
> > should have an intuitive name which highlights that in most cases,
> > _this_ is the right method for getting xrefs.
> >
> > get_all_DBEntries() is a special case which most users won't need, and
> > the name should indicate its nature as well (and maybe have a less
> > catchy name so that people don't use it by accident, as is the case
> > now).
> >
> > sure, all this is documented in the POD, but the beauty of the Ensembl
> > core API is that object and method names are so intuitive that in 95% of
> > the use cases you don't have to read the documentation. so, ironing out
> > the few wriggles would be cool.
> >
> > cheers
> >
> >    patrick
> >
> > --
> > Patrick Meidl, Mag.
> > Bioinformatician
> >
> > Ce-M-M-
> > Research Centre for Molecular Medicine
> > of the Austrian Academy of Science
> >
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> >
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> >
> >
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> >
> >
> 
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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom